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(-) Description

Title :  FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (DOMAIN G' AND V) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUND WITH EF-G AND GMPPCP, A NONHYDROLYSABLE GTP ANALOG
 
Authors :  R. K. Agrawal, J. Linde, J. Segupta, K. H. Nierhaus, J. Frank
Date :  07 Aug 01  (Deposition) - 07 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  NOT APPLICABLE
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  L11, Ef-G, Cryo-Em, 70S E. Coli Ribosome, Gtp State (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. K. Agrawal, J. Linde, J. Sengupta, K. H. Nierhaus, J. Frank
Localization Of L11 Protein On The Ribosome And Elucidation Of Its Involvement In Ef-G-Dependent Translocation.
J. Mol. Biol. V. 311 777 2001
PubMed-ID: 11518530  |  Reference-DOI: 10.1006/JMBI.2001.4907
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L11
    ChainsA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsL11 FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL STRUCTURE OF L11 FROM THERMATOGOMA MARITIMA
 
Molecule 2 - ELONGATION FACTOR G
    ChainsB
    FragmentPART OF DOMAIN G'
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsEF-G FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL STRUCTURE OF EF-G FROM THERMUS THERMOPHILUS
    SynonymEF-G;
TRANSLATION ELONGATION FACTOR EF-G
 
Molecule 3 - ELONGATION FACTOR G
    ChainsC
    FragmentDOMAIN V
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsEF-G FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL STRUCTURE OF EF-G FROM THERMUS THERMOPHILUS
    SynonymEF-G;
TRANSLATION ELONGATION FACTOR EF-G

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JQS)

(-) Sites  (0, 0)

(no "Site" information available for 1JQS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JQS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JQS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JQS)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_L11PS00359 Ribosomal protein L11 signature.RL11_THEMA126-141  1A:119-133

(-) Exons   (0, 0)

(no "Exon" information available for 1JQS)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:133
 aligned with RL11_THEMA | P29395 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:133
                                    17        27        37        47        57        67        77        87        97       107       117       127       137   
           RL11_THEMA     8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 140
               SCOP domains d1jqsa_ A: 70S ribosome functional complex                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jqs A   1 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:32
                                   229       239       249  
            EFG_THETH   220 AADFDENIMLKYLEGEEPTEEELVAAIRKGTI 251
               SCOP domains d1jqsb_ B:                       SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 1jqs B 220 AADFDENIMLKYLEGEEPTEEELVAAIRKGTI 251
                                   229       239       249  

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:68
                                   615       625       635       645       655       665        
            EFG_THETH   606 MRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFF 673
               SCOP domains d1jqsc_ C: 70S ribosome functional complex                           SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1jqs C 606 MRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFF 673
                                   615       625       635       645       655       665        

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1JQS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JQS)

(-) Gene Ontology  (16, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RL11_THEMA | P29395)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0070180    large ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0000027    ribosomal large subunit assembly    The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0022625    cytosolic large ribosomal subunit    The large subunit of a ribosome located in the cytosol.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain B,C   (EFG_THETH | P13551)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EFG_THETH | P135511efg 1fnm 1ip8 1ipm 1ipo 1ipr 1jqm 1ktv 1pn6 2bcw 2bm0 2bm1 2bv3 2efg 2j7k 2om7 3izp 4m1k 4myt 4myu
        RL11_THEMA | P293951eg0 1ip8 1jqm 1jqt 1mms 1mvr 1oln 1pn7 1pn8 1r2w 1r2x 2bcw 2gky 2gkz 2jq7 2k3f 487d

(-) Related Entries Specified in the PDB File

1eg0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME